Common germline variants of APOE contribute to differential COVID-19 outcomes

By Neha MathurReviewed by Danielle Ellis, B.Sc.Sep 26 2022

In a recent study published in Nature, researchers investigated the relationship between apolipoprotein E (APOE4) genotype and coronavirus disease 2019 (COVID-19) outcomes using genetic models of mice.

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection shows pronounced variation, ranging from asymptomatic infection to lethal disease. Moreover, multiple epidemiological studies have correlated male gender, old age, some comorbidities, and genetic makeup with adverse COVID-19 outcomes. Yet, there is a knowledge gap as to why there are wide variations in clinical outcomes of COVID-19 in humans. Hence, there is a crucial need to identify the factors underlying susceptibility to poor COVID-19 outcomes.

After concerted efforts, scientists found a significant correlation between germline genetics and COVID-19 severity. Subsequently, candidate gene approaches and genome-wide association (GWA) studies identified several genomic loci associated with severe COVID-19. However, the mechanism governing their effects remains unknown.

APOE modulates both innate and adaptive immunity in the context of pathogenic infections and cancers. It also plays a crucial role in lipid metabolism. Nearly 40% of the global population carries either APOE2 or APOE4 allele, while only 3% are homozygous for two other highly prevalent variants of APOE termed APOE2 or APOE4. It prompted the researchers to investigate the role of APOE allelic variants in causally modulating the outcomes of COVID-19, including susceptibility to death.

About the study

The present study used APOE knock-in mice with human APOE germline variations to determine whether APOE causally modulated SARS-CoV-2 infection in vivo. In addition, they gathered clinical association data via human studies to reinstate their findings in mice. They infected 328 APOE knock-in mice, having the murine APOE gene replaced with any of the human APOE genes, with a mouse-adapted (MA) 10 strain of SARS-CoV-2. Further, the researchers performed quantitative real-time polymerase chain reaction (PCR) on the lungs of APOE knock-in mice on day four post-infection (pi).

Furthermore, the researchers performed transcriptional profiling of homogenized lungs of non-infected APOE knock-in mice on days two and four pi. They also employed weighted gene co-expression network analysis (WGCNA) to identify clusters of closely correlated genes and compare their expression to genotype and timepoint relative to SARS-CoV-2 MA10 infection. Lastly, the team performed single-cell ribonucleic acid sequencing (scRNAseq) on 41,500 cells from 29 mice across all three genotypes with and without COVID-19.

Study findings

Among age-matched male and female mice, female mice showed higher survival overall. 100% of APOE4 mice died from COVID-19 relative to ~30% mortality in APOE3 mice, with a more severe impact in male mice. Expectedly, APOE2 and APOE4 mice showed elevated viral loads relative to APOE3 mice. APOE4 mice suffered more pronounced lung injuries, as observed in histopathological analyses on day four pi. Modules that exhibited downregulation in APOE2 and APOE4 mice relative to APOE3 on day four pi showed enrichment of genes implicated in T and B cell activation and positive immune response regulation.

Flow cytometry (FC) on dissociated lungs on day four pi further confirmed an expansion of myeloid cells and relative depletion of lymphoid cells in the lungs of APOE2 and APOE4 relative to APOE3 mice, indicating that the adaptive immune responses were blunted in APOE2 and APOE4 mice during early COVID-19 progression. Consistent with FC data, scRNAseq revealed expansion of myeloid cells in infected mice, which was more prominent in APOE2 and APOE4 relative to APOE3 mice.

Previous GWA studies could not spot an association between severe COVID-19 and APOE variations with any statistical significance. However, the researchers of the present study performed candidate gene analysis concomitantly with reverse genetic approaches to uncover two mechanisms underlying APOE-genotype-dependent variations in COVID-19 outcomes observed in mice. These findings also suggested a potential causal relationship between APOE4 genotypic variations and COVID-19 outcomes in humans.

During early SARS-CoV-2 infection, APOE2 and APOE4 mice showed impaired immune responses. However, during the later stages of COVID-19, APOE4 mice showed a divergent T cell antiviral response with increased expansion of SARS-CoV-2-specific CD8+ T cells. Relative to APOE3 and APOE4 mice, APOE2 mice had hyperactivated proinflammatory signaling, observed in single-cell transcriptional profiling.

Another mechanism noted by the researchers was that only recombinant APOE3 inhibited SARS-CoV-2 infection in vitro. A previous study similarly observed increased SARS-CoV-2 infection in APOE4 mice relative to neurons and astrocytes of APOE3 mice. However, the current study data interpreted it as the APOE3 allele repressing SARS-CoV-2 infection more than APOE2 and APOE4.

Conclusions

The study results have major clinical implications. Prospective clinical studies should determine whether APOE genotyping could be used for risk stratification in SARS-CoV-2 so that patients might benefit from early booster vaccinations, antiviral drugs, and monoclonal antibody therapies. Since common genetic variations, as with APOE genes, were shown to give rise to heterogeneous COVID-19 outcomes; therefore, it will be crucial to assess vaccination efficacy in individuals of distinct APOE genotypes.

APOE2 and APOE4 confer beneficial or detrimental outcomes in COVID-19, depending on the phenotype. Likewise, the APOE4 allele is the strongest monogenetic risk factor for Alzheimer’s disease. Further investigating these aspects could help researchers understand the neurocognitive changes imparted by COVID-19 and Alzheimer's. In other words, studies should further dissect how APOE variants have detrimental effects on COVID-19 outcomes at a molecular level.